What to know?

1. Basic R skills
2. Basic Unix/Linux skills

What to bring?

1. Bring laptop
2. A GitHub account?

Which R packages to install/load?

pkg <- c("ggplot2", "rmarkdown", "knitr", "dplyr");
lapply(pkg, function(x) { if (!require(x, character.only = TRUE, quietly = TRUE)) {
  install.packages(x);
  require(x, quietly = TRUE)}
})

What data to work with?

We will use the starwars dataset from dplyr.

head(starwars, n = 4);

## # A tibble: 4 x 13
##             name height  mass hair_color  skin_color eye_color birth_year
##            <chr>  <int> <dbl>      <chr>       <chr>     <chr>      <dbl>
## 1 Luke Skywalker    172    77      blond        fair      blue       19.0
## 2          C-3PO    167    75       <NA>        gold    yellow      112.0
## 3          R2-D2     96    32       <NA> white, blue       red       33.0
## 4    Darth Vader    202   136       none       white    yellow       41.9
## # ... with 6 more variables: gender <chr>, homeworld <chr>, species <chr>,
## #   films <list>, vehicles <list>, starships <list>

Create new R Markdown document in RStudio

1. File \(\rightarrow\) New File \(\rightarrow\) R Markdown

2. Specify output option

   

3. Render

1. Create a new R Markdown document in RStudio.
2. Select PDF, HTML and Word as output option.
3. Render the Markdown document to the corresponding output formats.
4. Locate and open the final output file.

Document conversion

1. Rmd -> PDF, HTML, Word uses rmarkdown::render() (knitr::pandoc() is deprecated)
2. rmarkdown::render() makes use of the universal document converter pandoc (installed as part of RStudio)

For example, pandoc will translate

# Header

into the following output-specific lines:

1. For HTML output

   <h1>Header</h1>

2. For \(\LaTeX\) output

   \section{Header}

Beware the different Markdown flavours: GitHub, R Markdown, vanilla Markdown, …

Focus here on R Markdown.

1. Headers
2. Emphasis: bold and italics
3. Lists: Ordered and unordered
4. Images and links
5. Blockquotes
6. Rules and line breaks

More details:

• Markdown basics
• R Markdown Cheat Sheet
• Markdown Cheat Sheet

1. Experiment with different markdown elements in your markdown document
2. Render the document and check the resulting output file
3. Are there any specific text elements you would like to typeset?

More options to include to include external images/figures.

1. Use ![](path/to/image.png)
2. Use HTML <img src="path/to/image.png" style="width:200px;">
3. Use knitr::include_graphics

1. Word
   [http://rmarkdown.rstudio.com/word_document_format.html]
2. PDF
   [http://rmarkdown.rstudio.com/pdf_document_format.html]
3. HTML
   [http://rmarkdown.rstudio.com/html_document_format.html]
4. Presentation (HTML, \(\LaTeX\) beamer)

---
title: "Main title"
subtitle: "Subtitle"
author: "Firstname Lastname"
date: "07/08/2017"
output:
  word_document
---

Main keys

1. Title and subtitle
2. Author (can have multiple authors as list for key author)
3. Date (can be R code, e.g. format(Sys.time(), '%d %B %Y'))
4. Output option: html_document, pdf_document, word_document, ioslides_presentation, beamer_presentation

Some useful options

• eval=FALSE: Don't run code.
• include=FALSE: Run code but don't include the chunk in the output document.
• echo=FALSE: Don't show code, show results.
• results='hide': Show code, don't show results.
• message=FALSE: Don't show any additional R messages.
• error=FALSE: Don't show R error messages.
• warning=FALSE: Don't show R warning messages.
• cache=TRUE: Use cached results (if available) until the code chunk is changed.
• fig.width=7, fig.height=7: Set figure width and height to 7 inches.

More chunk options can be found in e.g. the R Markdown Reference Guide.

1. General: How to output tables/dataframes?
2. knitr::kable()
3. tibble::print.tbl_df()
4. DT::datatable()

suppressMessages(library(knitr));
kable(starwars[1:4, 1:4])

suppressMessages(library(DT));
#DT::datatable(starwars, options = list(dom = "ftp", scrollX = TRUE, pageLength = 4));
DT::datatable(starwars[, 1:4], options = list(pageLength = 8));

1. plotly
2. D3 in R

Load the necessary libraries

suppressMessages(library(ggplot2));
suppressMessages(library(plotly));

## Warning: package 'plotly' was built under R version 3.4.1

suppressMessages(library(scatterD3));

ggplotly(ggplot(starwars, aes(x = height, y = mass, label = name)) + geom_point(), height = 5);

scatterD3(x = starwars$height, y = starwars$mass, lab = starwars$name);

R Markdown and shiny

…